Add Chikungunya parameters

inst/extdata/data_dictionary.json

@@ -20,7 +20,7 @@
         "description": "The name of the epidemiological distribution type. Names should be whitespace separated within each string.",
         "examples": ["incubation period", "serial interval", "offspring distribution"],
         "type": "string",
-        "enum": ["incubation period", "onset to hospitalisation", "onset to death", "serial interval", "generation time", "offspring distribution", "hospitalisation to death", "hospitalisation to discharge", "notification to death", "notification to discharge", "onset to discharge", "onset to ventilation"]
+        "enum": ["incubation period", "onset to hospitalisation", "onset to death", "serial interval", "generation time", "offspring distribution", "hospitalisation to death", "hospitalisation to discharge", "notification to death", "notification to discharge", "onset to discharge", "onset to ventilation", "case fatality risk"]
       },
       "probability_distribution": {
         "description": "An object containing the name of the probability distribution and its porameters if available.",

inst/extdata/parameters.json

@@ -11112,5 +11112,353 @@
     "phase_bias_adjusted": false
   },
   "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution"
+},
+{
+  "disease": "Chikungunya",
+  "pathogen": "Chikungunya Virus",
+  "epi_distribution": "generation time",
+  "probability_distribution": {
+    "prob_distribution": null,
+    "parameters": { }
+  },
+  "summary_statistics": {
+    "mean": 14,
+    "sd": 6.2
+  },
+  "citation": {
+    "author": [
+      {
+        "given": "Henrik",
+        "family": "Salje"
+      },
+      {
+        "given": "Simon",
+        "family": "Cauchemez"
+      },
+      {
+        "given": "Maria Theresa",
+        "family": "Alera"
+      },
+      {
+        "given": "Isabel",
+        "family": "Rodriguez-Barraquer"
+      },
+      {
+        "given": "Butsaya",
+        "family": "Thaisomboonsuk"
+      },
+      {
+        "given": "Anon",
+        "family": "Srikiatkhachorn"
+      },
+      {
+        "given": "Catherine B.",
+        "family": "Lago"
+      },
+      {
+        "given": "Daisy",
+        "family": "Villa"
+      },
+      {
+        "given": "Chonticha",
+        "family": "Klungthong"
+      },
+      {
+        "given": "Ilya A.",
+        "family": "Tac-An"
+      },
+      {
+        "given": "Stefan",
+        "family": "Fernandez"
+      },
+      {
+        "given": "John Mark",
+        "family": "Velasco"
+      },
+      {
+        "given": "Vito G.",
+        "family": "Roque Jr"
+      },
+      {
+        "given": "Ananda",
+        "family": "Nisalak"
+      },
+      {
+        "given": "Louis R.",
+        "family": "Macareo"
+      },
+      {
+        "given": "Jens W.",
+        "family": "Levy"
+      },
+      {
+        "given": "Derek",
+        "family": "Cummings"
+      },
+      {
+        "given": "In-Kyu",
+        "family": "Yoon"
+      }
+    ],
+     "title": "Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission",
+    "journal": "The Journal of Infectious Diseases",
+    "year": 2015,
+    "pmid": 26410592,
+    "doi": "10.1093/infdis/jiv470"
+  },
+  "metadata": {
+    "sample_size": null,
+    "region": "Philippines",
+    "transmission_mode": "vector_borne",
+    "vector": "mosquito",
+    "extrinsic": false,
+    "inference_method": null
+  },
+  "method_assessment": {
+    "truncation": null,
+    "discretised": false,
+    "censored": false,
+    "right_truncated": false,
+    "phase_bias_adjusted": false
+  },
+  "notes": "Database entry per communication K. Charniga, Z. Cucunubá & Laura Gomez Bermeo."
+},
+{
+    "disease": "Chikungunya",
+  "pathogen": "Chikungunya Virus",
+  "epi_distribution": "generation time",
+  "probability_distribution": {
+    "prob_distribution": "gamma",
+    "parameters": { }
+  },
+  "summary_statistics": {
+    "mean": 12.4,
+    "mean_ci_limits": [11.7, 13.3],
+    "mean_ci": 95,
+    "quantile_values": [5.6, 22.1],
+    "quantile_names": ["2.5", "97.5"]
+  },
+  "citation": {
+    "author": [
+      {
+        "given": "Giorgio",
+        "family": "Guzzetta"
+      },
+      {
+        "given": "Francesco",
+        "family": "Vairo"
+      },
+      {
+        "given": "Alessia",
+        "family": "Mammone"
+      },
+      {
+        "given": "Simone",
+        "family": "Lanini"
+      },
+      {
+        "given": "Piero",
+        "family": "Poletti"
+      },
+      {
+        "given": "Mattia",
+        "family": "Manica"
+      },
+      {
+        "given": "Roberto",
+        "family": "Rosa"
+      },
+      {
+        "given": "Beniamino",
+        "family": "Caputo"
+      },
+      {
+        "given": "Angelo",
+        "family": "Solimini"
+      },
+      {
+        "given": "Alessandra",
+        "family": "della Torre"
+      },
+      {
+        "given": "Paola",
+        "family": "Scognamiglio"
+      },
+      {
+        "given": "Alimuddin",
+        "family": "Zumla"
+      },
+      {
+        "given": "Giuseppe",
+        "family": "Ippolito"
+      },
+      {
+        "given": "Stefano",
+        "family": "Merler"
+      }
+    ],
+     "title": "Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis",
+    "journal": "BMC Medicine",
+    "year": 2020,
+    "pmid": 32762750,
+    "doi": "10.1186/s12916-020-01674-y"
+  },
+  "metadata": {
+    "sample_size": 412,
+    "region": "Italy",
+    "transmission_mode": "vector_borne",
+    "vector": "Aedes albopictus",
+    "extrinsic": false,
+    "inference_method": "bayesian"
+  },
+  "method_assessment": {
+    "truncation": null,
+    "discretised": false,
+    "censored": false,
+    "right_truncated": false,
+    "phase_bias_adjusted": false
+  },
+  "notes": "No additional notes."
+},
+{
+  "disease": "Chikungunya",
+  "pathogen": "Chikungunya Virus",
+  "epi_distribution": "case fatality risk",
+  "probability_distribution": {
+    "prob_distribution": null,
+    "parameters": { }
+  },
+  "summary_statistics": {
+    "mean": 1.3
+  },
+  "citation": {
+    "author": [
+      {
+        "given": "William M",
+        "family": "de Souza"
+      },
+      {
+        "given": "Shirlene T. S.",
+        "family": "de Lima"
+      },
+      {
+        "given": "Leda M Simões",
+        "family": "Mello"
+      },
+      {
+        "given": "Darlan S.",
+        "family": "Candido"
+      },
+      {
+        "given": "Lewis",
+        "family": "Buss"
+      },
+      {
+        "given": "Charles",
+        "family": "Whittaker"
+      },
+      {
+        "given": "Ingra M",
+        "family": "Claro"
+      },
+      {
+        "given": "Nilani",
+        "family": "Chandradeva"
+      },
+      {
+        "given": "Fabiana",
+        "family": "Granja"
+      },
+      {
+        "given": "Ronaldo",
+        "family": "de Jesus"
+      },
+      {
+        "given": "Poliana S.",
+        "family": "Lemos"
+      },
+      {
+        "given": "Daniel A.",
+        "family": "Toledo-Teixeira"
+      },
+      {
+        "given": "Priscilla P.",
+        "family": "Barbosa"
+      },
+      {
+        "given": "Antonio Carlos L.",
+        "family": "Firmino"
+      },
+      {
+        "given": "Mariene R.",
+        "family": "Amorim"
+      },
+      {
+        "given": "Larissa M. F.",
+        "family": "Duarte"
+      },
+      {
+        "given": "Ivan B.",
+        "family": "Pessoa Jr"
+      },
+      {
+        "given": "Julia",
+        "family": "Forato"
+      },
+      {
+        "given": "Irihane L.",
+        "family": "Vasconcelos"
+      },
+      {
+        "given": "Ana Carolina B. M.",
+        "family": "Maximo"
+      },
+      {
+        "given": "Emerson L. L.",
+        "family": "Araújo"
+      },
+      {
+        "given": "Liana Perdigão",
+        "family": "Mello"
+      },
+      {
+        "given": "Ester C.",
+        "family": "Sabino"
+      },
+      {
+        "given": "José Luiz",
+        "family": "Proença-Módena"
+      },
+      {
+        "given": "Nuno R.",
+        "family": "Faria"
+      },
+      {
+        "given": "Scott C.",
+        "family": "Weaver"
+      }
+    ],
+    "title": "Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study",
+    "journal": "The Lancet Microbe",
+    "year": 2023,
+    "pmid": 37031687,
+    "doi": "10.1016/S2666-5247(23)00033-2"
+  },
+  "metadata": {
+    "sample_size": 253545,
+    "region": "Brazil",
+    "transmission_mode": "vector_borne",
+    "vector": "Aedes aegypti and Aedes albopictus",
+    "extrinsic": false,
+    "inference_method": null
+  },
+  "method_assessment": {
+    "truncation": null,
+    "discretised": false,
+    "censored": true,
+    "right_truncated": false,
+    "phase_bias_adjusted": false
+  },
+  "notes": "Case fatality risk is given in deaths per 1,000 cases. It was calculated as a cumulative case fatality ratio. CFR is a population-wide estimate. Odds of chikungunya-related death were not significantly different between males and females. Odds of chikungunya-related death were significantly higher for 55-74 years old, and >75 years old compared to <18."
 }
 ]

tests/testthat/_snaps/parameter_tbl.md

@@ -4,7 +4,7 @@
       dist_tbl
     Output
       # Parameter table:
-      # A data frame:    122 x 7
+      # A data frame:    125 x 7
          disease  pathogen epi_distribution prob_distribution author  year sample_size
          <chr>    <chr>    <chr>            <chr>             <chr>  <dbl>       <dbl>
        1 Adenovi~ Adenovi~ incubation peri~ lnorm             Lessl~  2009          14
@@ -17,7 +17,7 @@
        8 Parainf~ Parainf~ incubation peri~ lnorm             Lessl~  2009          11
        9 RSV      RSV      incubation peri~ lnorm             Lessl~  2009          24
       10 Rhinovi~ Rhinovi~ incubation peri~ lnorm             Lessl~  2009          28
-      # i 112 more rows
+      # i 115 more rows
 
 # parameter_tbl works for incubation period with db